套件：freecontact（1.0.21-14） [debports]
fast protein contact predictor
FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).
FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.
A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.
jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.
This package contains the command line tool freecontact(1).
其他與 freecontact 有關的套件
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- dep: libboost-program-options1.83.0 (>= 1.83.0)
- program options library for C++
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- dep: libc6 (>= 2.38)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6-udeb
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- dep: libfreecontact0t64 (>= 1.0.21)
- fast protein contact predictor library
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- dep: libgcc-s2 (>= 4.2.1)
- GCC 支援函式庫
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- dep: libstdc++6 (>= 13.1)
- GNU Standard C++ Library v3
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- dep: libxerces-c3.2t64
- validating XML parser library for C++
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- dep: perl
- Larry Wall's Practical Extraction and Report Language
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- sug: bash-completion
- programmable completion for the bash shell
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- sug: hhsuite
- sensitive protein sequence searching based on HMM-HMM alignment
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- sug: hmmer
- profile hidden Markov models for protein sequence analysis